Transcription terminators are universal landmarks that delimit RNAs and tune downstream gene expression, yet the sequence rules that define them remain elusive. The classical model of bacterial intrinsic termination – an RNA hairpin followed by a uracil-rich tract – is incomplete, as stem-preserving mutations can abolish termination. By precisely mapping termination sites across 10^4 sequences, […]

Plasma proteomics has long sought to accessibly sense human biology, precisely detect disease states, and advance diagnostics through clinical translation. In recent years, companies with defined panels such as Olink and Somascan have entered the field to complement bottom-up mass spectrometry (BUP). This study leverages a novel mass spectrometry platform to capture targeted proteoform information […]

Accurate prioritization of T-cell receptor (TCR)-epitope interactions and identification of tumor-reactive T cells are important but difficult steps in immunotherapy-oriented bioinformatics workflows. Existing methods typically address these tasks separately and either model TCR-epitope pairs as independent observations or rely primarily on transcriptomic signatures. In this study, we present TRACE (TCR-epitope pRioritization And T-Cell idEntification), a […]

ProteomeLM is a proteome-scale language model trained on proteomes spanning the tree of life to reconstruct masked protein embeddings from proteome context within each species. Its attention coefficients capture protein-protein interactions without supervision. Here, we show that this capability extends to cross-species host-pathogen interactions (HPI) across ten human pathogen taxa spanning viruses and bacteria, and […]

Migraine headaches affect over one billion people internationally and can be defined as episodes of acute severe pain wrapping around the head and are normally accompanied by nausea, blurry vision, and sensitivity to light and sound. While triggers that cause migraines may vary among patients, evidence shows they are involved with the trigeminovascular system (a […]

Clear cell renal cell carcinoma (ccRCC) is characterized by transcriptional reprogram-ming driven by hypoxia signaling, metabolic rewiring, and immune modulation. While gene-level analyses have defined key features of ccRCC biology, they do not capture isoform-level variation arising from alternative splicing. Differential transcript usage (DTU) represents an additional regulatory layer that may influence protein function, pathway […]

Active-site redesign frequently yields modest improvements because residues controlling physical steps like substrate binding and product release lie outside the active site. Efficient catalysis requires a cooperative catalytic network of residues that support both the chemical and physical steps of catalysis. Using ancestral hydroxynitrile lyase HNL1, an /beta-hydrolase with poor esterase activity, we tested this […]

Since Darwin’s time, ultra-slow oscillatory movements have been recognized as a characteristic feature of axis elongation in plant organs such as shoots and tendrils, yet have not been reported in elongating animal body axes. Here, using long-term imaging of multiple anesthetized Xenopus laevis embryos with a modified document scanner, we identify a previously unrecognized ultra-slow […]

Plant-associated microbiomes help sustain plant immunity and productivity, yet the degree to which agricultural antimicrobials reshape these microbial networks and alter disease outcomes remains poorly characterized. Here, we quantified how chemical inputs such as copper and streptomycin trigger distinct, compartment-specific dysbiosis in tomato (Solanum lycopersicum), fundamentally decoupling microbiome-mediated immunity from pathogen defense. We demonstrated that […]

Germline variants in DDX41 are the most frequent genetic predisposition to adult hematologic malignancies. The most common variants are truncating, implicating loss of function in the pathogenesis. However, non-truncating variants account for 30-40% of cases, and their impact on essential DDX41 functions remains unknown. We utilized a genetic complementation assay to assess the functionality of […]

Small interfering RNAs (siRNAs) have become a transformative class of nucleic acid therapeutics for clinical disease treatment, yet sequence-dependent off-target silencing continues to pose a major safety barrier that hinders their preclinical refinement and large-scale translational application. Existing bioinformatics tools only support partial off-target evaluation, either focusing on basic sequence optimization or simple seed-region scanning, […]